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git clone https://github.com/bichangwei/PMAT.git
cd PMAT/bin
chmod a+x PMAT
PMAT --help

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wget https://github.com/bichangwei/PMAT/archive/refs/tags/v1.5.2.tar.gz
tar -zxvf v1.5.2.tar.gz
cd PMAT-1.5.2/bin
chmod a+x PMAT
PMAT --help

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usage: PMAT <command> <arguments>

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PMAT            An efficient assembly toolkit for plant mitochondrial genome
Version         1.5.2
Contributors    Bi,C. and Han,F.
Email           bichwei@njfu.edu.cn, hanfc@caf.ac.cn

For more information about PMAT, please see https://github.com/bichangwei/PMAT

optional arguments:
-h, --help     show this help message and exit
-v, --version  show program's version and exit

Commands:

    autoMito    One-step de novo assembly of the mitochondrial genome. 
                This command can generate the master assembly graph 
                from raw sequencing data directly.

    graphBuild  If 'autoMito' mode fails to generate the mitogenome 
                assembly graph, you can use this command to manually 
                select seeds for assembly.

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Required arguments:
  -i INPUT, --input INPUT
                        input raw sequencing file
  -o OUTPUT, --output OUTPUT
                        output directory
  -st SEQTYPE, --seqtype SEQTYPE
                        sequencing platform(ONT/CLR/HiFi)
  -g GENOMESIZE, --genomesize GENOMESIZE
                        Please enter the genome size of the species, such as 1G, 1000M.

optional arguments:
  -h, --help            show this help message and exit
  -tk TASK, --task TASK
                        all/p1/ Default: all
                        all : De novo assembly including error correction for ONT/CLR data and no error correction for HiFi data
                        p1  : Import error-corrected ONT/CLR data for direct assembly
  -tp TYPE, --type TYPE
                        mt/pt/all Default: mt
                        mt   : Assembling the mitochondrial genome
                        pt   : Assembling the chloroplast genome
                        all  : Assembling the mitochondrial and chloroplast genomes
  -cs CORRECTSOFT, --correctsoft CORRECTSOFT
                        Correcting software using nextDenovo or Canu. Default: NextDenovo
  -cp CANU, --canu CANU
                        Please provide the install path of canu.
  -np NEXTDENOVO, --nextDenovo NEXTDENOVO
                        Please provide the install path of nextDenovo.
  -cfg CORRECTCFG, --correctcfg CORRECTCFG
                        config file for nextdenovo correct
  -fc FACTOR, --factor FACTOR
                        Subset extraction of error-corrected ONT, CLR or HiFi data. Sampling ratio factor in 0-1. Default: 1
  -sd SUBSEED, --subseed SUBSEED
                        Sampling set random number seeds, Default: 6
  -bn BREAKNUM, --breaknum BREAKNUM
                        break long reads (>30k) with this. Default: 20000
  -ml MINOVERLAPLEN, --minoverlaplen MINOVERLAPLEN
                        set minimum overlap length. Default: 40
  -mi MINIDENTITY, --minidentity MINIDENTITY
                        set minimum overlap identification. Default: 90
  -cpu CPU              The number of threads. Default: 8
  -l MINLINK, --minLink MINLINK
                        Filter according to the minimum link depth provided by the user
  -m, --mem             Flag to keep sequence data in memory to speed up cup time
  -u, --unloop          Flag for attempting automatic unloop
  -v, --version         show program's version and exit

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Required arguments:
  -c CONTIGGRAPH, --ContigGraph CONTIGGRAPH
                        PMATContigGraph.txt: a file that can get all connections between contigs.
  -a ALLCONTIGS, --AllContigs ALLCONTIGS
                        PMATAllContigs.fna: a file that can get all the information of contigs.
  -o OUTPUT, --output OUTPUT
                        output directory
  -gs GENOMESIZE, --genomesize GENOMESIZE
                        Please enter the genome size of the species, such as 1G, 1000M.
  -rs READSIZE, --readsize READSIZE
                        The read size or file for assembly, such as 5G or assembly_seq.cut20K.fasta.

optional arguments:
  -h, --help            show this help message and exit
  -tp TYPE, --type TYPE
                        mt/pt/all Default: mt
                        mt   : Assembling the mitochondrial genome
                        pt   : Assembling the chloroplast genome
                        all  : Assembling the mitochondrial and chloroplast genomes
  -cpu CPU              The number of threads. Default: 8
  -s SEEDS [SEEDS ...], --seeds SEEDS [SEEDS ...]
                        ContigID for extending. Multiple contigIDs should be separated by space. For example: 1 312 356
  -u, --unloop          Flag for attempting automatic unloop
  -l MINLINK, --minLink MINLINK
                        Filter according to the minimum link depth provided by the user
  -v, --version         show the program's version number and exit